This study is part of a 15-year project to develop less invasive methods to diagnose pneumocystis pneumonia and to predict responses to therapy. Oral washes, induced sputum, and bronchalveolar lavage are being collected from patients with immunosuppressive diseases and respiratory syndromes. Samples for control patients are being collected as well. First, a polymerase chain reaction (PCR) technique using a unique major surface glycoprotein primer is being used in conjunction with a published primer to develop a method adaptable to clinical laboratories that is highly specific and sensitive. It is hoped that oral wash can replace sputum as the sample of choice. Second, mutations associated with drug resistance are being assessed in all organisms identified to determine the epidemiology and clinical importance of such mutations. Third, markers of strain variation are being assessed to elucidate pathogen epidemiology. Specimens are being obtained from NIH and the Washington Hospital Center. Results from 30 patients with morphologic evidence of PCP, and 250 smear-negative immunosuppressed patients show that the oral wash has a 70 percent positive-predictive value and a 99 percent negative-predictive value. The oral wash, tested by PCR, is a useful screening test for PCP. This will be published in the Journal of Infectious Diseases. A quantitative assay has been developed to increase the positive-predictive value of this test. This technique (Journal of Clinical Microbiology, in press) separates colonized patients from those with disease. A prospective study assessing this quantitative test is in progress in collaboration with UCSF.